BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WeNMR
IntroductionwithTALOS+andCYANApractical

HenryJonker

CenterforBiomolecularMagneticResonance(BMRZ)
InstituteforOrganicChemistryandChemicalBiology
GoetheUniversity FrankfurtamMain(Germany)

WeNMRapplicationsontheGrid HenryJonker(2013)

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WeNMR
Projectconsortium:whoandwhatisWeNMR?

IntroductiontotheGrid
Registration,CertficatesandVirtualOrganisation
Middlewarecomponentsandsecurity

WeNMR
Infrastructure
Applications
Webportals

Practical
Talosprediction
Cyanastructure
calculation

2
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WeNMR
ProvidecomputationalapplicationsandresourcesnecessaryforNMRandSAXSdata
processing,analysis,structurecalculations,docking,refinementandmodelling.
EUfundedproject(followupofeNMR,20072010)
ExtendstheuseofBiomolecularNMRandSAXSresearchinfrastructures

( )

NMR

SAXS

( EU-NMR )

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WeNMRprojectconsortium
BijvoetCenterforBiomolecularResearch(BCBR)
UtrechtUniversity,TheNetherlands
CenterforBiomolecularMagneticResonance(BMRZ)
GoetheUniversity,FrankfurtamMain,Germany
InteruniversityConsortiumforMagneticResonanceonMetalloproteins(CIRMMP)
UniversityofFlorence,Italy
NationalInstituteofNuclearPhysics(INFN)
DepartmentofPhysicsGalileoGalilei,Padova,Italy
ProteinBiophysics,IMMandCMBI,NCMLS
RadboudUniversityNijmegen,TheNetherlands
BiochemistryDepartment,UniversityofCambridge(UCAM)
CambridgeUniversity,Cambridge,UK
EuropeanMolecularBiologyLaboratory(EMBL)
HamburgOutstation,Hamburg,Germany
SpronkNMRConsultancy(SpronkNMR) Vilnius,Lithuania
AcademiaSinica(AS) Taipei,Taiwan

4
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WhyusingWeNMR?
Largevarietyofapplicationsiseasilyavailableviauserfriendlywebportals
Comparedifferentcomputationalsoftwareapproacheswithminimal effort
Workflowandintegrationofstructuralbiologyapplications
Noneedforcomplicatedsoftwareinstallationandmaintenance
Obtainexperiencewithuptodateadvancedstructuralmethods
Accesstothe(hidden)computationalresourcesoftheGrid
ProvidedbylargeNMRandGridfacilitiesinEurope
Collaborationswithmanyotherprojects
Supportedallovertheworld
website:www.wenmr.eu

Usersupport:
VirtualResearchCommunity(VRC)
HelpCentre,Tutorials,Wiki,Forums
WeNMRuserscomefromstructural
biology,life &escienceandindustry

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

TheGrid
Connectsdistributedcomputerclusters
Securilysharedresources
Highperformancedistributedcomputing

InternationalGridTrustFederation(IGTF)
PolicyManagementAuthority(PMA)forEurope,AsiaPacificandAmerica

NationalGridInitiatives(NGIs)
Managethecomputingresourcesofeachcountry

InternationalGridCollaborations
EuropeanGridinfrastructures:
EnablingGridsforESciencE(EGEEIIII,20042010)
EuropeanGridInitiative(EGI,since2011)
GridInitiativesforeSciencevirtualcommunitiesin
EuropeandLatinAmerica(gisela)
OpenScienceGrid,BalticGrid,EUAsiaGrid,....

6
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WhoisusingtheGrid?
Userswithdemandingapplications
Needforhighcomputationalpower
Needforlargeamountsofdatastorage

UsersareorganisedinVirtualOrganisations(VOs)
sharecommonresourcesofthegroup

Manydifferentresearchareas
Astronomy,Fusion,QuantumComputing
HighEnergyPhysics,Geophysics
EarthSciences,Weatherforecast
FinancialSimulation
Mathematics,Statistics,Cryptography
LifeSciences,MolecularBiology,
Computational(bio)chemistry
Multimedia
MaterialSciences,Nanotechnology

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

SecurityontheGrid:
PersonalcertificatesanduserregistrationtoVOs
Authentication:WhoareweontheGrid?
Authorization:Accessallowedtospecificresources&services?
Protection:Dataintegrity&confidentiality!

CertificationAuthority (CA)
Userpersonalcertificate&privatekey Useridentified
(passport)by
RegistrationAuthority
GridUser VOm (RA)oftheNGI
e mber
ship
VOmanager User
Map
database pin g
VO
quest
Proxyre

UserInterface (UI) Access Grid

orwebportal services&resources

8
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

TheGridcomputationalinfrastructure
CentralMiddlewareServices:
Forsubmission,management,security,storage,
execution,monitoringandbookkeeping
gLitemiddleware(20052010)
EuropeanMiddlewareInitiative(EMI,since2011)
andUnifiedMiddlewareDistribution(UMD)
JobssubmittedtoaWorkloadManagementSystem(WMS)
checkauthenticationandvalidity(proxy,certifacate,VO)
LoggingandBookkeeping(LB)servicekeepstrackofthejobstatusandevents
Forwardjobtoan(assigned)ComputingElement(CE)
Sitequeuingsystemforsubmission&executiononworkernodes(WNs)

CE1 WNs

RegisteredUser
WMS/LB CE2.. WNs
atUIorwebportal

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

Additionalservices:availableintheenmr.euGrid

StorageElement(SE)supplementedwithdataencryptionkeystores(HYDRA)for
security&protectionofsensitiveuserinformation
VirtualOrganisationMembershipService(VOMS)
GlobalGridUserSupport(GGUS)
DiverseMonitoring,databaseandaccountingservices:
BerkelyDatabaseInformationIndex(BDII),RelationalGridMonitoringArchitecture(RGMA)
withAccountingProcessorforEventLogs(APEL)andaDistrubutedGridAccountingSystem
(DGAS)HomeLocationRegister(HLR),LCGFileCatalog(LFC),Gstat,Nagios,...

DGAS-HLRmon Grid-PP RTM

10
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

Theenmr.euGridinfrastructure

CentralservicesdistributedamongthepartnersandsupportedbymanyNGIs
TheNetherlands: BCBR,BigGrid,NIKHEF,SARA,Belgium(BEgrid):ULBVUB,KULeuven
Germany(NGIDE): BMRZFRANKFURT,DESYHH,FZKLCG2,UK: SCOTGRID,GridPP,RALL
Italy(IGI): CIRMMP,INFN*,CNR*,GARR,Portugal(INGRID): UMinhoCP,Spain(ESNGI)
France(Grilles): OBSPM
OutsideEurope:
GISELAproject: Argentina: EELAUNLP,Brazil(CEFET/RJ): UFRJIF,CBPF,Venezuela(ULA)
China(IHEP):BEIJINGLCG2 andTaiwan(TWGrid)
SouthAfrica(SAGrid): NWU,UCTICTS,UJ
Malaysia(AcademicGrid):UPMBIRUNI,

LargestVOinLifeSciencesarea
28Gridsites(statisticsApril2013)
64.000cpucores,250TBstorage
544registeredusersworldwide
(35%outsideEurope)

11

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WeNMRWebportalservices:
StructurecalculationandModelling
CYANA
CSRosetta
UNIO
XplorNIH
ASDP
Modelling
HADDOCK
3DDART
Processing
MDDNMR
MolecularDynamics
Amber,Gromacs
Assignment
MARS,AutoAssign
Analysisandtools
Talos+,AniosFIT,MaxOcc,RPF,
iCing,Formatconverter,ShiftX2,
Antechamber,DisMeta,Fandas
Preditor,RCI,Uplabel,sedNMR
12
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

AdvantageofWeNMRcomputingontheGrid

ExampleCSRosetta
Applicationforthecalculationofa
3DstructurebasedonNMRchemical
shiftinformation,usingaSPARTAbased
fragmentselectionprocedure.

HighlyCPUintensive!
averagerunon1CPU(5000CPUhours):~200days
samerunonGrid(dependingontheload):~12days

13

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

TALOS+andCYANA
practicalontheWeNMRGrid
HenryJonker

CenterforBiomolecularMagneticResonance(BMRZ)
InstituteforOrganicChemistryandChemicalBiology
GoetheUniversity FrankfurtamMain(Germany)

PracticaluseoftheWeNMRwebportalsTALOS+andCYANA HenryJonker(2013)

14
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

WeNMRWebportals

visit:www.wenmr.eu

15

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

TALOS+ prediction

useschemicalshiftdataof threeconsecutiveresidues(triplet)topredict the backbone

torsionanglesofthecentralresidue
databaseofbackbonetorsionanglesderivedfromwelldefinedpartsof200protein
Xraystructureswith13C,13C,13C,1H and15Nand1HN chemicalshiftassignments
INPUT:proteinsequenceandexperimentalchemicalshiftvalues
(psi)

180
OUTPUT:predicted (phi)and (psi)torsionangles
90 l
0

-90
-180
HN H HN H HN H -180 -90 0 90 180
(phi)
N C C' N C C' N C C'

C O C O C O C C

Ri1 Ri Ri+1

16
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

RunningTALOS+

fromtheWeNMRwebsitemenu:NMRservices/Analysis/TALOS+

checktheinputNapDtalos.tabfile
givetherunaname,selecttheNapDtalos.tabfile(TALOStype)

submitthequery

17

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

RunningTALOS+

afterthejobhasfinished(typicallyafterafewseconds)thewebpagegetsupdatedwith
alinktoretrievetheresults:

inspectandtrytounderstandtheresults
downloadandsavethetalos.acorestraintfileforusewiththeCYANAcalculation
editthefiletoremovetheprolinephianglerestraints(prolines30and40)

18
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

SetupofaCYANArun

RunacompleteautomatedNOEassignmentandstructurecalculationoftheNapD
proteinwithCYANA
Availabledata:
1H13CNOESYHSQC(aliphatic) NapD13CALI.peaks
1H13CNOESYHSQC(aromatic) NapD13CARO.peaks
1H15NNOESYHSQC(amides) NapD15N.peaks
Chemicalshiftassignment NapD.prot
NapDproteinsequence NapD.seq
backbonetorsionanglesfromTALOS+ talos.aco
Carefullycheckandunderstandtheinputfiles

fromtheWeNMRwebsitemenu:NMRservices/StructureCalculation/CYANA

19

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

RunningCYANA

Inputfiles
sequence:NapD.seq
nodistancebounds
torsionangles:talos.aco
orwithout(dotworuns)

Settings
50structures,10final
5000steps
corerange476

Calculationtype
unassignedpeaklists

20
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

RunningCYANA

Peaklists
tolerance:0.03,0.03,0.45
automaticcalibration:clear
nodistancelimits:clear

Chemicalshiftlist
NapD.prot

Peaklists
NapD13CALI.peaks
NapD13CARO.peaks
NapD15N.peaks

Enterusername/password
andsubmit(notedowntheJobid)

21

BMRZ
FrankfurtamMain

www.bmrz.unifrankfurt.de
Goethe University

Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

Retrieveandanalysetheresults

Theproceduretakesabout4560minutes(cyanarunandjobsubmissions)
prerunsareavailable(folders:output_cyana&output_cyana_notalos)
Retrievetheresultsandunpack(tarxzvfoutput_cyana.tgz)

CyanaproducesoutputandstatisticsforeachofthecyclesofautomatedNOE
assignmentandstructurecalculations.Importantoutputfilesare:
NOA possibleandusedNOEpeakassignmentsandquality.
UPL listoftheupperlimitdistancerestraints(ambiguousassignmentsarelisted
insubsequentlines notpresentinthelastcycleandfinalstructurecalculation)
PDB containthecoordinatesofthestructuremodelsinPDBformat
OVW overviewofstructuralstatistics,RMSDandrestrainviolations
CYANATABLE overviewofthestatisticsforallcyclesandthefinalcalcuation

Inspectthestructures(molmol/pymol)andthestatistics.
Checktheconvergenceandthenumberofpeakassignmentsinthedifferentclasses.
Makeajudgementofthesuccesofeachrun(withandwithoutdihedralanglerestraints).

22
 BMRZ

FrankfurtamMain
www.bmrz.unifrankfurt.de

Goethe University
Network ofResearchInfrastructures
www.wenmr.eu providingAccess and Technological
www.bionmr.net Advancements inBiomolecularNMR HenryJonker
BiomolecularNMR

NapD

ThankstoSpronkNMR
http://www.spronknmr.eu/

Exampledataderivedfrom:
Structuraldiversityintwinargininesignalpeptidebindingproteins
MaillardJ,SpronkCAEM,BuchananG,LyallV,RichardsonDJ,PalmerT,VuisterGW,SargentF

23